Merge pull request #5 from Breeding-Insight/revert-develop-merge

Revert "Merge pull request #4 from Breeding-Insight/develop"

Author: nickpalladino

.github/workflows/docker-build.yml

@@ -6,146 +6,59 @@ on:
       - develop
       - release/**
       - brapi-server-v2
-
+      
   workflow_dispatch:
-    inputs:
-      upstream_repo:
-        description: 'Optional: Override upstream repository (owner/repo). Defaults to the repository this was forked from if not set.'
-        required: false
-        default: 'plantbreeding/brapi-Java-ProdServer'
-      upstream_pr_number:
-        description: 'Required if merging an upstream PR: PR number from the upstream repository to merge into develop for this build. ex: 11'
-        required: false # Still false overall, but logic will require it if this feature is used.
-        type: string
 
 jobs:
   docker:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout branch
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0 # Fetch all history to ensure common ancestor is found
-
-      - name: Conditionally Fetch and Merge Upstream PR
-        # This step runs if a PR number is provided AND (an upstream_repo input is given OR a parent repo full_name is available)
-        if: |
-          github.event.inputs.upstream_pr_number &&
-          github.event.inputs.upstream_repo
-        run: |
-          UPSTREAM_REPO_SPECIFIED="${{ github.event.inputs.upstream_repo }}"
-          UPSTREAM_PR_NUMBER="${{ github.event.inputs.upstream_pr_number }}"
-
-          if [[ -z "$UPSTREAM_PR_NUMBER" ]]; then
-            echo "No upstream PR number provided. Skipping PR merge."
-            exit 0
-          fi
-
-          TARGET_UPSTREAM_REPO=""
-          if [[ -n "$UPSTREAM_REPO_SPECIFIED" ]]; then
-            TARGET_UPSTREAM_REPO="$UPSTREAM_REPO_SPECIFIED"
-            echo "Using specified upstream repository: $TARGET_UPSTREAM_REPO"
-          else
-            echo "Error: Upstream PR number '$UPSTREAM_PR_NUMBER' was provided, but no upstream_repo was specified and parent repository could not be determined."
-            exit 1
-          fi
-
-          echo "Upstream PR to merge: $UPSTREAM_PR_NUMBER from $TARGET_UPSTREAM_REPO"
-          UPSTREAM_REPO_URL="https://github.com/$TARGET_UPSTREAM_REPO.git"
-
-          # Fetch the PR from the upstream repository
-          git fetch $UPSTREAM_REPO_URL +refs/pull/$UPSTREAM_PR_NUMBER/head:upstream_pr_branch
-
-          echo "Fetched PR branch 'upstream_pr_branch'. Merging into current HEAD (develop)..."
-          # Merge the fetched PR branch. If conflicts occur, the script will exit with an error.
-          git config user.name "GitHub Actions"
-          git config user.email "actions@github.com"
-          git merge upstream_pr_branch --no-ff -m "Merge upstream PR #$UPSTREAM_PR_NUMBER from $TARGET_UPSTREAM_REPO for testing"
-
-          echo "Merge complete."
-        shell: bash
-
+      - uses: actions/checkout@v2
+      
       - name: Extract branch name
         shell: bash
-        run: echo "branch=$(echo ${GITHUB_REF#refs/heads/})" >> "$GITHUB_OUTPUT"
+        run: echo ::set-output name=branch::$(echo ${GITHUB_REF#refs/heads/})
         id: extract_branch
-
-      # This pull is no longer needed as checkout handles fetching the correct ref,
-      # and the PR merge step brings in specific upstream changes.
-      # - run: git pull origin ${{steps.extract_branch.outputs.branch}}
-
+        
+      - run: git pull origin ${{steps.extract_branch.outputs.branch}}
+      
       - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
           distribution: temurin
           java-version: '21'
           cache: maven
-
+          
       - name: Build with Maven
         run: mvn clean install
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v2
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@v2
         with:
-          platforms: 'arm64,arm,amd64'
-
+          platforms: 'arm64,arm,amd64,amd'        
+        
       - name: Login to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
-
-      - name: Determine Docker Tags
-        id: docker_tags
-        shell: bash
-        run: |
-          PR_NUMBER="${{ github.event.inputs.upstream_pr_number }}"
-          IMAGE_BASE_NAME="breedinginsight/brapi-java-server"
-          TAGS=""
-          IS_PR_BUILD="false"
-
-          if [[ -n "$PR_NUMBER" ]]; then
-            echo "This is a PR build. Setting PR-specific tag."
-            PR_TAG="$IMAGE_BASE_NAME:pr-$PR_NUMBER"
-            TAGS="$PR_TAG"
-            IS_PR_BUILD="true"
-          else
-            echo "This is a regular build. Setting standard tags."
-            RUN_NUMBER_TAG="$IMAGE_BASE_NAME:${{ github.run_number }}"
-            TAGS="$RUN_NUMBER_TAG"
-
-            BRANCH_NAME="${{ steps.extract_branch.outputs.branch }}"
-            STREAM_NAME=""
-            if [[ "$BRANCH_NAME" == "develop" ]]; then
-              STREAM_NAME="$IMAGE_BASE_NAME:develop"
-            elif [[ "$BRANCH_NAME" == "brapi-server-v2" ]]; then # Assuming brapi-server-v2 is 'latest'
-              STREAM_NAME="$IMAGE_BASE_NAME:latest"
-            elif [[ "${{ github.ref }}" == refs/heads/release/* ]]; then
-              STREAM_NAME="$IMAGE_BASE_NAME:rc"
-            fi
-
-            if [[ -n "$STREAM_NAME" ]]; then
-              TAGS="$TAGS,$STREAM_NAME" # Comma-separated for docker/build-push-action
-            fi
-          fi
-          echo "Final tags: $TAGS"
-          echo "tags=$TAGS" >> "$GITHUB_OUTPUT"
-          echo "is_pr_build=$IS_PR_BUILD" >> "$GITHUB_OUTPUT"
-
-      # The original 'Set tag' and 'Tag develop/rc/latest' steps are now incorporated into 'Determine Docker Tags'
-      # and are conditioned by is_pr_build logic within that step.
+      - name: Set tag
+        id: vars
+        run: echo ::set-output name=imageName::$(echo breedinginsight/brapi-java-server:${{ github.run_number }})
+        
+      - name: Tag develop
+        if: steps.extract_branch.outputs.branch == 'develop'
+        run: echo "streamName=breedinginsight/brapi-java-server:develop" >> $GITHUB_ENV
+      - name: Tag release candidate
+        if: contains(github.ref, '/release/')
+        run: echo "streamName=breedinginsight/brapi-java-server:rc" >> $GITHUB_ENV
+      - name: Tag latest
+        if: steps.extract_branch.outputs.branch == 'brapi-server-v2'
+        run: echo "streamName=breedinginsight/brapi-java-server:latest" >> $GITHUB_ENV
 
       - name: Build Docker and push image
         run: |
-          # Note: The `docker/build-push-action` is generally recommended over manual scripting
-          # as it handles tags more robustly. However, to keep the change minimal,
-          # this script adapts the original logic.
-          FORMATTED_TAGS=""
-          IFS=',' read -ra TAG_ARRAY <<< "${{ steps.docker_tags.outputs.tags }}"
-          for tag in "${TAG_ARRAY[@]}"; do
-            FORMATTED_TAGS="$FORMATTED_TAGS --tag $tag"
-          done
-          docker buildx build . --file Dockerfile $FORMATTED_TAGS --push --platform=linux/arm64,linux/amd64
+          docker buildx build . --file Dockerfile --tag ${{steps.vars.outputs.imageName}} --tag ${{env.streamName}} --push --platform=linux/arm64,linux/amd64

src/main/java/org/brapi/test/BrAPITestServer/controller/pheno/ObservationsApiController.java

@@ -121,7 +121,7 @@ public ResponseEntity<ObservationSingleResponse> observationsObservationDbIdPut(
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_USER");
 		validateAcceptHeader(request);
-		Observation data = observationService.updateObservationAndConvert(observationDbId, body);
+		Observation data = observationService.updateObservation(observationDbId, body);
 		return responseOK(new ObservationSingleResponse(), data);
 	}
 

src/main/java/org/brapi/test/BrAPITestServer/model/dto/ObservationUnitGermplasmData.java

@@ -3,12 +3,23 @@
 import jakarta.persistence.*;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
 
-@Embeddable
-public class ExperimentalDesignEntity {
-	@Column(name = "pui", table = "study_experimental_design")
+@Entity
+@Table(name = "study_experimental_design")
+public class ExperimentalDesignEntity extends BrAPIBaseEntity {
+	@Column
 	private String PUI;
-    @Column(name = "description", table = "study_experimental_design")
+	@Column
 	private String description;
+	@OneToOne(fetch = FetchType.LAZY)
+	private StudyEntity study;
+
+    public StudyEntity getStudy() {
+        return study;
+    }
+
+    public void setStudy(StudyEntity study) {
+        this.study = study;
+    }
 
     public String getPUI() {
         return PUI;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ExperimentalDesignEntity.java

@@ -3,12 +3,23 @@
 import jakarta.persistence.*;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
 
-@Embeddable
-public class GrowthFacilityEntity {
-	@Column(name = "pui", table = "study_growth_facility")
+@Entity
+@Table(name = "study_growth_facility")
+public class GrowthFacilityEntity extends BrAPIBaseEntity {
+	@Column
 	private String PUI;
-	@Column(name = "description", table = "study_growth_facility")
+	@Column
 	private String description;
+	@OneToOne(fetch = FetchType.LAZY)
+	private StudyEntity study;
+
+    public StudyEntity getStudy() {
+        return study;
+    }
+
+    public void setStudy(StudyEntity study) {
+        this.study = study;
+    }
 
     public String getPUI() {
         return PUI;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/GrowthFacilityEntity.java

@@ -12,11 +12,6 @@
 
 @Entity
 @Table(name = "study")
-@SecondaryTables({
-        @SecondaryTable(name = "study_experimental_design", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id")),
-        @SecondaryTable(name = "study_growth_facility", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id")),
-        @SecondaryTable(name = "study_last_update", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id"))
-})
 @Where(clause = "soft_deleted = false")
 public class StudyEntity extends BrAPIPrimaryEntity {
 
@@ -37,11 +32,11 @@ public class StudyEntity extends BrAPIPrimaryEntity {
 	private Date endDate;
 	@OneToMany(mappedBy = "study")
 	private List<EnvironmentParametersEntity> environmentParameters;
-	@Embedded
+	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
 	private ExperimentalDesignEntity experimentalDesign;
-	@Embedded
+	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
 	private GrowthFacilityEntity growthFacility;
-	@Embedded
+	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
 	private StudyLastUpdateEntity lastUpdate;
 	@Column
 	private String license;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyEntity.java

@@ -5,12 +5,23 @@
 
 import java.util.Date;
 
-@Embeddable
-public class StudyLastUpdateEntity {
-	@Column(name = "timestamp", table = "study_last_update")
+@Entity
+@Table(name = "study_last_update")
+public class StudyLastUpdateEntity extends BrAPIBaseEntity {
+	@Column
 	private Date timestamp;
-	@Column(name = "version", table = "study_last_update")
+	@Column
 	private String version;
+	@OneToOne(fetch = FetchType.LAZY)
+	private StudyEntity study;
+
+    public StudyEntity getStudy() {
+        return study;
+    }
+
+    public void setStudy(StudyEntity study) {
+        this.study = study;
+    }
 
     public Date getTimestamp() {
         return timestamp;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyLastUpdateEntity.java

@@ -10,7 +10,6 @@
 import org.brapi.test.BrAPITestServer.model.entity.germ.CrossEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.SeedLotEntity;
-import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Where;
 
 import java.util.List;
@@ -29,7 +28,6 @@ public class ObservationUnitEntity extends BrAPIPrimaryEntity {
 	private String observationUnitPUI;
 	@ManyToOne(fetch = FetchType.LAZY)
 	private SeedLotEntity seedLot;
-	@BatchSize(size = 50)
 	@OneToMany(mappedBy="observationUnit", cascade=CascadeType.ALL)
 	private List<TreatmentEntity> treatments;
 	@OneToOne(mappedBy="observationUnit", cascade=CascadeType.ALL, fetch = FetchType.LAZY)
@@ -42,7 +40,6 @@ public class ObservationUnitEntity extends BrAPIPrimaryEntity {
 	private TrialEntity trial;
 	@ManyToOne(fetch = FetchType.LAZY)
 	private StudyEntity study;
-	@BatchSize(size = 50)
 	@OneToMany(mappedBy="observationUnit", cascade=CascadeType.ALL, fetch = FetchType.LAZY)
 	private List<ObservationEntity> observations;
 

src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitEntity.java

@@ -3,7 +3,6 @@
 import java.io.Serializable;
 import java.util.List;
 import java.util.Optional;
-import java.util.UUID;
 
 import org.brapi.test.BrAPITestServer.exceptions.InvalidPagingException;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
@@ -31,7 +30,7 @@ public interface BrAPIRepository<T extends BrAPIPrimaryEntity, ID extends Serial
 
 	public <S extends T> void refresh(S entity);
 
-	public void fetchXrefs(List<UUID> page, Page<T> pagedEntities, Class<T> searchClass) throws InvalidPagingException;
+	public void fetchXrefs(Page<T> page, Class<T> searchClass) throws InvalidPagingException;
 
 	List<T> findByIdIn(List<ID> ids);
 }

src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepository.java

@@ -14,7 +14,6 @@
 import org.brapi.test.BrAPITestServer.exceptions.InvalidPagingException;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
 import org.brapi.test.BrAPITestServer.model.entity.ExternalReferenceEntity;
-import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
 import org.brapi.test.BrAPITestServer.service.SecurityUtils;
 
@@ -142,17 +141,17 @@ public <S extends T> void refresh(S entity) {
 		this.entityManager.refresh(entity);
 	}
 
-	public void fetchXrefs(List<UUID> ids, Page<T> pagedEntities, Class<T> searchClass) {
-		SearchQueryBuilder<T> searchQuery = new SearchQueryBuilder<>(searchClass);
+	public void fetchXrefs(Page<T> page, Class<T> searchClass) throws InvalidPagingException {
+		SearchQueryBuilder<T> searchQuery = new SearchQueryBuilder<T>(searchClass);
 		searchQuery.leftJoinFetch("externalReferences", "externalReferences")
-				   .appendIds(ids);
+				   .appendList(page.stream().map(p -> p.getId().toString()).collect(Collectors.toList()), "id");
 
-		List<T> xrefs = findAllBySearch(searchQuery);
+		Page<T> xrefs = findAllBySearchAndPaginate(searchQuery, PageRequest.of(0, page.getSize()));
 
 		Map<UUID, List<ExternalReferenceEntity>> xrefByEntity = new HashMap<>();
 		xrefs.forEach(entity -> xrefByEntity.put(entity.getId(), entity.getExternalReferences()));
 
-		pagedEntities.forEach(entity -> entity.setExternalReferences(xrefByEntity.get(entity.getId())));
+		page.forEach(entity -> entity.setExternalReferences(xrefByEntity.get(entity.getId())));
 	}
 
 	private void applyUserId(SearchQueryBuilder<T> searchQuery) {